Segregation of QTL for production traits in commercial meat-type chickens

This study investigated whether quantitative trait loci (QTL) identified in experimental crosses of chickens provide a short cut to the identification of QTL in commercial populations. A commercial population of broilers was targeted for chromosomal regions in which QTL for traits associated with meat production have previously been detected in extreme crosses. A three-generation design, consisting of 15 grandsires, 608 half-sib hens and over 15 000 third-generation offspring, was implemented within the existing breeding scheme of a broiler breeding company. The first two generations were typed for 52 microsatellite markers spanning regions of nine chicken chromosomes and covering a total of 730 cM, approximately one-fifth of the chicken genome. Using half-sib analyses with a multiple QTL model, linkage was studied between these regions and 17 growth and carcass traits. Out of 153 trait x region comparisons, 53 QTL exceeded the threshold for genome-wide significance while an additional 23 QTL were significant at the nominal 1% level. Many of the QTL affect the carcass proportions and feed intake, for which there are few published studies. Given intensive selection for efficient growth in broilers for more than 50 generations it is surprising that many QTL affecting these traits are still segregating. Future fine-mapping efforts could elucidate whether ancestral mutations are still segregating as a result of pleiotropic effects on fitness traits or whether this variation is due to new mutations.     

A genome scan for loci affecting adipocyte size and number in abdominal fat in a White Duroc × Erhualian F2 resource population

Adipocyte size and number are correlated with fat deposition, which is of major concern to human health and pork producers. To identify quantitative trait loci (QTL) for adipocyte size and number in pigs, a total of 341 F2 animals at 240 days in a White Duroc × Erhualian cross were measured for the area, perimeters, volume and number of adipocyte in abdominal fat. A genome scan was performed on these animals and their parents and grandparents with 183 microsatellite markers spanning the pig genome. Five chromosomal regions showed effects on the traits measured, predominantly on adipocyte size, on pig chromosome (SSC) 1, 4, 7 and 9. Neither of these QTL has been reported before this study. The QTL for adipocyte size detected in this study perfectly correspond to the previously reported QTL for fatness traits on SSC1, 4 and 7. The most significant association was evidenced at 58 cM on SSC7. At the locus, the favorable allele decreasing adipocyte size was unusually originated from the obese Erhualian breed. Only a suggestive QTL was detected for adipocyte number on SSC9. The results shed new lights on the understanding of the genetic basis of fatness traits in pigs.     

QTL affecting fleece traits in Angora goats

With the aim to detect chromosome segment (quantitative traits loci, QTL) affecting fleece traits in Angora goats, a genome scan using 76 microsatellite markers spanning 1261 cM on 21 chromosomes was conducted. Eight paternal half-sib families were used, which included a total of 288 kids from a dispersed nucleus herd.Mid-side mohair samples were taken from kids at 4 months of age and eight phenotypic fleece traits were measured.We found putatives QTL for coefficient of variation of average fiber diameter (CVAFD) in chromosome 1 and 13, for kemp fiber (KEMP) in chromosome 5 and for discontinuous medullated fibers (DISC) and staple length (SL) in chromosome 2.These results demonstrate the segregation of quantitative traits involved in mohair production. Further studies will concentrate on these regions to characterize the variation of these QTL.     

Mapping quantitative trait loci affecting chicken body size traits via genome scanning

Body size traits reflect the condition of body development, are always mentioned when a breed is described, and are also targets in breeding programmes. In chicken, there are several reports focused on body size traits, such as shank length, tibia length or bone traits. However, no study was carried out on chest width (CW), chest depth (CD), body slope length (BL) and head width (HW) traits. In this study, genome scans were conducted on an F₂ resource population (238 F₂ individuals from 15 full‐sib families derived from an intercross of the White Plymouth Rock with the Silkies Fowl) to identify quantitative trait loci (QTL) associated with CW, CD, BL and HW from 7 to 12 weeks of age. In total, 21 significant or suggestive QTL were found that affected four body size traits. Four QTL reached 1% genome‐wide significance level: at 297 cM on GGA3 (associated with CW at 9 weeks of age), between 155 and 184 cM on GGA1 (affecting BL traits at 9 and 10 weeks of age), at 22 cM on GGA2 (related with BL traits at 12 weeks of age) and at 36 cM on GGA1 (for HW trait at 8 weeks of age).     

Genome wide QTL mapping to identify candidate genes for carcass traits in Hanwoo (Korean Cattle)

Meat quality traits are the most economically important traits affecting the beef industry in Korea. We performed a whole genome quantitative trait locus (QTL) mapping study of carcass data in Hanwoo Korean cattle. Two hundred sixty-six Hanwoo steers from 65 sires were genotyped using a 10K Affymetrix SNP chip. The average SNP interval across the bovine genome was 1.5Mb. Associations between each individual SNP and four carcass traits [carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling (MAR)] were assessed using a linear mixed model of each trait. Combined linkage and linkage disequilibrium analysis (LDLA) detected six potential QTL on BTA04, 06, 13, 16, 17, and 23 at the chromosome-wise level (P<0.05). Two MAR QTL were detected at 52.2 cM of BTA06 and 46.04 cM of BTA17. We identified three genes (ARAP2, LOC539460, and LOC511424) in the QTL region of BTA06 and seven genes (RPS14, SCARB1, LOC782103, BRI3BP, AACS, DHX37, and UBC) in the QTL region of BTA17. One significant QTL for CWT was detected at 100 cM on BTA04 and the corresponding QTL region spanned 1.7 cM from 99.7 to 101.4 cM. For EMA QTL, one significant QTL was detected at 3.9 cM of BTA23 and the most likely QTL interval was 1.4 cM, placing 15 candidate genes in the marker bracket. Finally, two QTL for BFT were identified at 68 cM on BTA13 and 24 cM on BTA16. The LPIN3 gene, which is functionally associated with lipodystrophy in humans, is located in the BFT QTL on BTA13. Thus, two potential candidate genes, acetoacetyl-CoA synthetase (AACS) and lipin (LPIN), were detected in QTL regions on BTA17 for MAR and BTA13 for BFT, respectively. In conclusion, LDLA analysis can be used to detect chromosome regions harboring QTL and candidate genes with a low density SNP panel, yielding relatively narrow confidence intervals regarding location.     

Construction of High-Density Genetic Linkage Maps and Mapping of Growth-Related Quantitative Trail Loci in the Japanese Flounder (Paralichthys olivaceus)

High-density genetic linkage maps were constructed for the Japanese flounder (Paralichthys olivaceus). A total of 1624 microsatellite markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 resulted in the mapping of 1487 markers to 24 linkage groups, a result which was consistent with the 24 chromosomes seen in chromosome spreads. The female map was composed of 1257 markers, covering a total of 1663.8 cM with an average interval 1.35 cM between markers. The male map consisted of 1224 markers, spanning 1726.5 cM, with an average interval of 1.44 cM. The genome length in the Japanese flounder was estimated to be 1730.3 cM for the females and 1798.0 cM for the males, a coverage of 96.2% for the female and 96.0% for the male map. The mean recombination at common intervals throughout the genome revealed a slight difference between sexes, i.e. 1.07 times higher in the male than female. High-density genetic linkage maps are very useful for marker-assisted selection (MAS) programs for economically valuable traits in this species and for further evolutionary studies in flatfish and vertebrate species. Furthermore, four quantiative trait loci (QTL) associated with growth traits were mapped on the genetic map. One QTL was identified for body weight on LG 14 f, which explained 14.85% of the total variation of the body weight. Three QTL were identified for body width on LG14f and LG14m, accounting for 16.75%, 13.62% and 13.65% of the total variation in body width, respectively. The additive effects were evident as negative values. There were four QTL for growth traits clustered on LG14, which should prove to be very useful for improving growth traits using molecular MAS.     

Characterization of variation and quantitative trait loci related to terpenoid indole alkaloid yield in a recombinant inbred line mapping population of <Emphasis Type="Italic">Catharanthus roseus</Emphasis>

Improved Catharanthus roseus cultivars are required for high yields of vinblastine, vindoline and catharanthine and/or serpentine and ajmalicine, the pharmaceutical terpenoid indole alkaloids. An approach to derive them is to map QTL for terpenoid indole alkaloids yields, identify DNA markers tightly linked to the QTL and apply marker assisted selection. Towards the end, 197 recombinant inbred lines from a cross were grown over two seasons to characterize variability for seven biomass and 23 terpenoid indole alkaloids content-traits and yield-traits. The recombinant inbred lines were genotyped for 178 DNA markers which formed a framework genetic map of eight linkage groups (LG), spanning 1786.5 cM, with 10.0 cM average intermarker distance. Estimates of correlations between traits allowed selection of seven relatively more important traits for terpenoid indole alkaloids yields. QTL analysis was performed on them using single marker (regression) analysis, simple interval mapping and composite interval mapping procedures. A total of 20 QTL were detected on five of eight LG, 10 for five traits on LG1, five for four traits on LG2, three for one trait on LG3 and one each for different traits on LG three and four. QTL for the same or different traits were found clustered on three LG. Co-location of two QTL for biomass traits was in accord of correlation between them. The QTL were validated for use in marker assisted selection by the recombinant inbred line which transgressively expressed 16 traits contributory to the yield vinblastine, vindoline and catharanthine from leaves and roots that possessed favourable alleles of 13 relevant QTL.     

Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement

A comprehensive analysis was conducted using 48 sorghum QTL studies published from 1995 to 2010 to make information from historical sorghum QTL experiments available in a form that could be more readily used by sorghum researchers and plant breeders. In total, 771 QTL relating to 161 unique traits from 44 studies were projected onto a sorghum consensus map. Confidence intervals (CI) of QTL were estimated so that valid comparisons could be made between studies. The method accounted for the number of lines used and the phenotypic variation explained by individual QTL from each study. In addition, estimated centimorgan (cM) locations were calculated for the predicted sorghum gene models identified in Phytozome (JGI GeneModels SBI v1.4) and compared with QTL distribution genome-wide, both on genetic linkage (cM) and physical (base-pair/bp) map scales. QTL and genes were distributed unevenly across the genome. Heterochromatic enrichment for QTL was observed, with approximately 22% of QTL either entirely or partially located in the heterochromatic regions. Heterochromatic gene enrichment was also observed based on their predicted cM locations on the sorghum consensus map, due to suppressed recombination in heterochromatic regions, in contrast to the euchromatic gene enrichment observed on the physical, sequence-based map. The finding of high gene density in recombination-poor regions, coupled with the association with increased QTL density, has implications for the development of more efficient breeding systems in sorghum to better exploit heterosis. The projected QTL information described, combined with the physical locations of sorghum sequence-based markers and predicted gene models, provides sorghum researchers with a useful resource for more detailed analysis of traits and development of efficient marker-assisted breeding strategies.     

Analysis of an intraspecific RIL population uncovers genomic segments harbouring multiple QTL for seed relevant traits in lentil (<Emphasis Type="Italic">Lens culinaris</Emphasis> L.)

Improving seed related traits remains key objective in lentil breeding. In recent years, genomic resources have shown great promise to accelerate crop improvement. However, limited genomic resources in lentil greatly restrict the use of genomics assisted breeding. The present investigation aims to build an intraspecific genetic linkage map and identify the QTL associated with important seed relevant traits using 94 recombinant inbreds (WA 8649090 × Precoz). A total of 288 polymorphic DNA markers including simple sequence repeat (SSR), inter simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) were assayed on mapping population. The resultant genetic linkage map comprised 220 loci spanning 604.2 cM of the lentil genome, with average inter-marker distance of 2.74 cM. QTL mapping in this RIL population uncovered a total of 18 QTL encompassing nine major and nine minor QTL. All major QTL were detected for seed related traits viz., seed diameter (SD), seed thickness (ST), seed weight (SW) and seed plumpness (SP) across two locations. A considerable proportion of the phenotypic variation (PV) was accounted to these QTL. For instance, one major QTL on LG5 controlling SW (QTL 15) explained 50% PV in one location, while the same QTL accounted for 34.18% PV in other location. Importantly, the genomic region containing multiple QTL for different seed traits was mapped to a 17-cM region on LG5. The genomic region harbouring QTL for multiple traits opens up exciting opportunities for genomics assisted improvement of lentil.     

QTL analysis of yield traits in an advanced backcross population derived from a cultivated Andean × wild common bean (Phaseolus vulgaris L.) cross

Advanced backcross QTL analysis was used to identify quantitative trait loci (QTL) for agronomic performance in a population of BC₂F_3:5 introgression lines created from the cross of a Colombian large red-seeded commercial cultivar, ICA Cerinza, and a wild common bean accession, G24404. A total of 157 lines were evaluated for phenological traits, plant architecture, seed weight, yield and yield components in replicated trials in three environments in Colombia and genotyped with microsatellite, SCAR, and phaseolin markers that were used to create a genetic map that covered all 11 linkage groups of the common bean genome with markers spaced at an average distance of every 10.4 cM. Segregation distortion was most significant in regions orthologous for a seed coat color locus (R-C) on linkage group b08 and two domestication syndrome genes, one on linkage group b01 at the determinacy (fin) locus and the other on linkage group b02 at the seed-shattering (st) locus. Composite interval mapping analysis identified a total of 41 significant QTL for the eight traits measured of which five for seed weight, two for days to flowering, and one for yield were consistent across two or more environments. QTL were located on every linkage group with b06 showing the greatest number of independent loci. A total of 13 QTL for plant height, yield and yield components along with a single QTL for seed size showed positive alleles from the wild parent while the remaining QTL showed positive alleles from the cultivated parent. Some QTL co-localized with regions that had previously been described to be important for these traits. Compensation was observed between greater pod and seed production and smaller seed size and may have resulted from QTL for these traits being linked or pleiotropic. Although wild beans have been used before to transfer biotic stress resistance traits, this study is the first to attempt to simultaneously obtain a higher yield potential from wild beans and to analyze this trait with single-copy markers. The wild accession was notable for being from a unique center of diversity and for contributing positive alleles for yield and other traits to the introgression lines showing the potential that advanced backcrossing has in common bean improvement.     

Genome-wide identification of quantitative trait loci for carcass composition and meat quality in a large-scale White Duroc × Chinese Erhualian resource population

Carcass and meat quality traits are economically important in pigs. In this study, 17 carcass composition traits and 23 meat quality traits were recorded in 1028 F₂ animals from a White Duroc × Erhualian resource population. All pigs in this experimental population were genotyped for 194 informative markers covering the entire porcine genome. Seventy-seven genome-wide significant quantitative trait loci (QTL) for carcass traits and 68 for meat quality were mapped to 34 genomic regions. These results not only confirmed many previously reported QTL but also revealed novel regions associated with the measured traits. For carcass traits, the most prominent QTL was identified for carcass length and head weight at 57 cM on SSC7, which explained up to 50% of the phenotypic variance and had a 95% confidence interval of only 3 cM. Moreover, QTL for kidney and spleen weight and lengths of cervical vertebrae were reported for the first time in pigs. For meat quality traits, two significant QTL on SSC5 and X were identified for both intramuscular fat content and marbling score in the longissimus muscle, while three significant QTL on SSC1 and SSC9 were found exclusively for IMF. Both LM and the semimembranous muscle showed common QTL for colour score on SSC4, 5, 7, 8, 13 and X and discordant QTL on other chromosomes. White Duroc alleles at a majority of QTL detected were favourable for carcass composition, while favourable QTL alleles for meat quality originated from both White Duroc and Erhualian.     

Genetic Mapping and QTL Analysis of Growth-Related Traits in the Pacific Oyster

The Pacific oyster (Crassostrea gigas) is one of the most important oysters cultured worldwide. To analyze the oyster genome and dissect growth-related traits, we constructed a sex-averaged linkage map by combining 64 genomic simple sequence repeats, 42 expressed sequence tag-derived SSRs, and 320 amplified fragment length polymorphism markers in an F₁ full-sib family. A total of 426 markers were assigned to 11 linkage groups, spanning 558.2 cM with an average interval of 1.3 cM and 94.7% of genome coverage. Segregation distortion was significant for 18.8% of the markers (P < 0.05), and distorted markers tended to occur on some genetic regions or linkage groups. Most growth-related quantitative traits were highly significantly (P < 0.01) correlated, and principal component analysis obtained four principal components. Quantitative trait locus (QTL) analysis identified three significant QTLs for two principal components, which explained 0.6–13.9% of the phenotypic variation. One QTL for sex was detected on linkage group 6, and the inheritabilities of sex for parental alleles and maternal alleles on that locus C15 are 39.8% and 0.01%, respectively. The constructed linkage map and determined QTLs can provide a tool for further genetic analysis of the traits and be potential for marker-assisted selection in C. gigas breeding.     

Mapping QTLs for morpho-agronomic traits in proso millet (<Emphasis Type="Italic">Panicum miliaceum</Emphasis> L.)

Proso millet (Panicum miliaceum L.) is the cereal crop with the low water requirement and increasingly being used for human consumption. It is the most common rotational crop within wheat-based dryland production systems in the semiarid High Plains of the USA. However, there is no published genetic map for this species, which prevents the identification of quantitative trait loci (QTL). The objectives of the present study were (1) construction of a genetic linkage map and (2) identification of DNA markers linked to QTLs for morpho-agronomic traits. A total of 93 recombinant inbred lines derived from a single F₁ (“Huntsman” × “Minsum”) were genotyped with GBS-SNP markers and phenotyped for nine morpho-agronomic traits in the field during 2013 and 2014 at Scottsbluff and Sidney, NE. IciMapping v.4.0.6.0 was used for constructing a genetic linkage map and mapping QTL. The RILs exhibited significant variation for a wide range of traits, and several traits showed evidence of genotype × environment interactions. A total of 833 GBS-SNP markers formed 18 major and 84 minor linkage groups, whereas 519 markers remained ungrouped. A total of 117 GBS-SNP markers were distributed on the 18 major linkage groups spanning a genome length of 2137 cM of proso millet with an average distance of 18 cM between markers. The length and number of markers in each of the 18 major linkage groups ranged from 54.6 to 236 cM and 4 to 12, respectively. A total of 18 QTLs for eight morpho-agronomic traits were detected on 14 linkage groups, each of which explained 13.2–34.7 % phenotypic variance. DNA markers flanking the QTLs were identified, which will aid in marker-assisted selection of these traits. To our knowledge, this is the first genetic linkage map and QTL mapping in proso millet, which will support further genetic analysis and genomics-assisted genetic improvement of this crop.     

Linkage analysis and identification of quantitative trait loci associated with freeze tolerance and turf quality traits in St. Augustinegrass

St. Augustinegrass [Stenotaphrum secundatum (Walt.) Kuntze] is a warm-season turfgrass commonly grown in the southern USA. In this study, the first linkage map for all nine haploid chromosomes of the species was constructed for cultivar ‘Raleigh’ and cultivar ‘Seville’ using a pseudo-F₂ mapping strategy. A total of 160 simple sequence repeat markers were mapped to nine linkage groups (LGs) covering a total distance of 1176.24 cM. To demonstrate the usefulness of the map, quantitative trait loci (QTL) were mapped controlling field winter survival, laboratory-based freeze tolerance, and turf quality traits. Multiple genomic regions associated with these traits were identified. Moreover, overlapping QTL were found for winterkill and spring green up on LG 3 (99.21 cM); turf quality, turf density, and leaf texture on LG 3 (68.57–69.50 cM); and surviving green tissue and regrowth on LGs 1 (38.31 cM), 3 (77.70 cM), 6 (49.51 cM), and 9 (34.20 cM). Additional regions, where QTL identified in both field and laboratory-based/controlled environment freeze testing co-located, provided strong support that these regions are good candidates for true gene locations. These results present the first complete linkage map produced for St. Augustinegrass, providing a template for further genetic mapping. Additionally, markers linked to the QTL identified may be useful to breeders for transferring these traits into new breeding lines and cultivars.     

Mapping QTL for grain yield, yield components, and spike features in a doubled haploid population of bread wheat

A doubled haploid (DH) population derived from a cross between the Japanese cultivar 'Fukuho-kumogi' and the Israeli wheat line 'Oligoculm' was used to map genome regions involved in the expression of grain yield, yield components, and spike features in wheat (Triticum aestivum L). A total of 371 markers (RAPD, SSR, RFLP, AFLP, and two morphological traits) were used to construct the linkage map that covered 4190 cM of wheat genome including 28 linkage groups. The results of composite interval mapping for all studied traits showed that some of the quantitative trait loci (QTL) were stable over experiments conducted in 2004 and 2005. The major QTL located in the Hair-Xpsp2999 interval on chromosome 1A controlled the expression of grains/spike (R(2) = 12.9% in 2004 and 22.4% in 2005), grain weight/spike (R(2) = 21.4% in 2004 and 15.8% in 2005), and spike number (R(2) = 15.6% in 2004 and 5.4% in 2005). The QTL for grain yield located on chromosomes 6A, 6B, and 6D totally accounted for 27.2% and 31.7% of total variation in this trait in 2004 and 2005, respectively. Alleles inherited from 'Oligoculm' increased the length of spikes and had decreasing effects on spike number. According to the data obtained in 2005, locus Xgwm261 was associated with a highly significant spike length QTL (R(2) = 42.33%) and also the major QTL for spikelet compactness (R(2) = 26.1%).     

Identification of QTLs for eight agronomically important traits using an ultra-high-density map based on SNPs generated from high-throughput sequencing in sorghum under contrasting photoperiods

The productivity of sorghum is mainly determined by agronomically important traits. The genetic bases of these traits have historically been dissected and analysed through quantitative trait locus (QTL) mapping based on linkage maps with low-throughput molecular markers, which is one of the factors that hinder precise and complete information about the numbers and locations of the genes or QTLs controlling the traits. In this study, an ultra-high-density linkage map based on high-quality single nucleotide polymorphisms (SNPs) generated from low-coverage sequences (~0.07 genome sequence) in a sorghum recombinant inbred line (RIL) population was constructed through new sequencing technology. This map consisted of 3418 bin markers and spanned 1591.4 cM of genome size with an average distance of 0.5 cM between adjacent bins. QTL analysis was performed and a total of 57 major QTLs were detected for eight agronomically important traits under two contrasting photoperiods. The phenotypic variation explained by individual QTLs varied from 3.40% to 33.82%. The high accuracy and quality of this map was evidenced by the finding that genes underlying two cloned QTLs, Dw3 for plant height (chromosome 7) and Ma1 for flowering time (chromosome 6), were localized to the correct genomic regions. The close associations between two genomic regions on chromosomes 6 and 7 with multiple traits suggested the existence of pleiotropy or tight linkage. Several major QTLs for heading date, plant height, numbers of nodes, stem diameter, panicle neck length, and flag leaf width were detected consistently under both photoperiods, providing useful information for understanding the genetic mechanisms of the agronomically important traits responsible for the change of photoperiod.     

High resolution mapping of chromosomal regions controlling resistance to gastrointestinal nematode infections in an advanced intercross line of mice

Fine mapping of quantitative trait loci (QTL) associated with resistance to the gastrointestinal parasite Heligmosomoides polygyrus was achieved on F₆/F₇ offspring (1076 mice) from resistant (SWR) and susceptible (CBA) mouse strains by selective genotyping (top and bottom 20% selected on total worm count in week 6). Fecal egg counts were recorded at weeks 2, 4, and 6, and the average was also analyzed. Blood packed cell volume in weeks 3 and 6 and five immunological traits (mucosal mast cell protease 1, granuloma score, IgG1 against adult worm, IgG1, and IgE to L4 antigen) were also recorded. On Chromosome 1 single-trait analyses identified a QTL with effects on eight traits located at about 24 cM on the F₂ mouse genome database (MGD) linkage map, with a 95% confidence interval (CI) of 20-32 cM established from a multitrait analysis. On Chromosome 17 a QTL with effects on nine traits was located at about 18 cM on the MGD map (CI 17.9-18.4 cM). Strong candidate genes for the QTL position on Chromosome 1 include genes known to be involved in regulating immune responses and on Chromosome 17 genes within the MHC, notably the Class II molecules and tumor necrosis factor.     

Analysis of candidate genes underlying two epistatic quantitative trait loci on SSC12 affecting litter size in pig

The previous results from a genome scan for total number of piglets born and number of piglets born alive in a F₂ Iberian by Meishan intercross showed several single and epistatic QTL. One of the most interesting results was obtained for SSC12, where two QTL affecting both traits showed epistatic interaction. In this study, we proposed two genes ( SLC9A3R1 and NOS2 ) as biological and potentially positional candidates underlying these QTL. Both cDNAs were characterized and 23 polymorphisms were detected. A chromosome scan was conducted with 12 markers, plus one SNP in SLC9A3R1 and one in NOS2, covering 110 cM of SSC12. The epistatic QTL (QTL1 at 15 cM and QTL2 at 97 cM) were confirmed, and SLC9A3R1 and NOS2 were mapped around the QTL1 and QTL2 regions respectively. Several SNPs in both genes were tested with standard animal model and marker assisted association tests. The most significant results were obtained with the NOS2 haplotype defined by one missense SNP c.2192C > T (Val to Ala) and a 15 bp duplication at the 3'UTR. This duplication seems to include AU-rich elements, and could be a target site for miRNA, therefore there are statistical and biological indications to consider this haplotype as the potential causal mutation underlying QTL2. SLC9A3R1 results were not conclusive. Although the interaction between the SNPs was not significant, we cannot reject the possibility of interaction of the NOS2 haplotype with other polymorphisms closely linked to the SL9A3R1 SNPs analysed.     

A genome scan for loci affecting pork quality in a Duroc-Landrace F population

A genome scan was conducted on 370 F2 Duroc-Landrace pigs. Microsatellite markers (n = 182) were genotyped across the entire F2 population, all F1 parents and the paternal grandparents. Breed of origin of all chromosomal segments inherited in F2 progeny were predicted using GenoProb, where genotypic data, genetic maps and extended pedigrees were used as inputs. Statistical tests for quantitative trait loci (QTL) associations were conducted on 41 phenotypes with SAS using output from GenoProb for genotypic data. Fixed effects included sex and age at slaughter. For certain analyses carcass weight, RYR1 genotype and/or PRKAG3 genotype were also included as covariates. Subjective and objective measures of pork colour, marbling and tenderness were recorded, as well as measures of carcass fatness and muscularity. Test results were adjusted to a genome-wide level of significance. Five genomic regions presented significant evidence for QTL at chromosome 1 positions 6 cM (intramuscular fat) and 67 cM (Hunter L*), chromosome 2 position 62 cM (taste panel tenderness), chromosome 17 position 50 (loineye area and image analysis estimated loineye area) and X position 87 cM (carcass weight). Sixty-six suggestive associations were detected. Fourteen of these associations were within the regions with significant QTL on chromosomes 2, 17 and X, and the remaining 52 associations resided in 29 other regions on 13 different chromosomes of the porcine genome. The chromosome 2 region of 60-66 cM was associated with all measures of pork tenderness and the region on chromosome 17 (32-39 cM) was associated with both measures of intramuscular fat and loineye area. After verification, the QTL for marbling and tenderness should be useful in commercial production to improve pork quality as the population was developed from two of the three most utilized breeds of swine in the USA.